D. W. Yu

Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies

The paper uses eDNA surveys to infer metacommunity assembly processes in ponds and finds environmental factors and species interactions shape community composition.

Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity

The paper combines environmental DNA and remote sensing to map arthropod biodiversity at fine spatial scales, revealing patterns in species richness and conservation value.

Extracting abundance information from DNA-based data

The paper addresses biases in DNA-based data to improve within-species abundance estimation using spike-ins and a model-based estimator.

Biodiversity Soup II: A bulk-sample metabarcoding pipeline emphasizing error reduction

This paper introduces a metabarcoding pipeline to reduce errors in bulk-sample sequencing, showing reduced false positives and biases but no recovery of relative-abundance information.

Climate-induced forest dieback drives compositional change in insect communities that is concentrated amongst rare species

The paper investigates the impact of climate-induced forest dieback on insect communities, finding compositional changes driven by rare species rather than salvage logging.

Competition-based screening secures the evolutionary stability of a defensive microbiome

The paper shows that competition-based screening by Pseudonocardia symbionts maintains a stable defensive microbiome in Acromyrmex ants by eliminating non-antibiotic-producing microbes.

Measuring protected-area outcomes with leech iDNA: large-scale quantification of vertebrate biodiversity in Ailaoshan reserve

The paper quantifies vertebrate biodiversity in Ailaoshan reserve using leech iDNA, showing species richness increases with elevation and distance from the reserve edge.

Environmental DNA facilitates accurate, indigenous-led, inexpensive, and multi-year population estimates of millions of Eulachon fish

This study shows that environmental DNA (eDNA) can accurately estimate eulachon fish populations over multiple years, with high predictive power compared to mark-recapture methods, at a lower cost.

Semi-quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)

This paper introduces RevMet, a pipeline for semi-quantitative characterization of mixed eukaryote samples using MinION sequencing and genome skims, demonstrating its effectiveness in identifying plant species in pollen samples.

Environmental DNA for the enumeration and management of Pacific salmon

This study demonstrates that flow-corrected environmental DNA (eDNA) rates can accurately track daily numbers of returning and outmigrating Pacific salmon spawners and smolts.

Shifting up a gear with iDNA: from mammal detection events to standardized surveys

The paper compares iDNA and camera-trap surveys to assess mammal occupancy in tropical rainforests, finding consistent results and suggesting iDNA as a viable complementary method.

Using eDNA to Detect the Distribution and Density of Invasive Crayfish in the Honghe-Hani Rice Terrace World Heritage Site

This study tests eDNA detection for invasive crayfish in rice terraces, finding it more sensitive than trapping and suggesting repeated sampling for reliable monitoring.